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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 2557 IN COMPLEX WITH AN NOF V3 PEPTIDE
 
Authors :  X. -P. Kong
Date :  18 Apr 10  (Deposition) - 14 Jul 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  H,L,M,N,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  M,N,Q  (1x)
Keywords :  Human Monoclonal Antibody, Fab, Hiv-1, Gp120, Third Variable Loop, Antibody-Antigen Interaction, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Jiang, V. Burke, M. Totrov, C. Williams, T. Cardozo, M. K. Gorny, S. Zolla-Pazner, X. P. Kong
Conserved Structural Elements In The V3 Crown Of Hiv-1 Gp120.
Nat. Struct. Mol. Biol. V. 17 955 2010
PubMed-ID: 20622876  |  Reference-DOI: 10.1038/NSMB.1861

(-) Compounds

Molecule 1 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 2557 FAB LIGHT CHAIN
    Chains: L, M
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 2557 FAB HEAVY CHAIN
    Chains: H, N
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HIV-1 GP120 THIRD VARIABLE REGION (V3) CROWN
    Chains: P, Q
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HLMNPQ
Biological Unit 1 (1x): HL  P 
Biological Unit 2 (1x):   MN Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3MLV)

(-) Sites  (0, 0)

(no "Site" information available for 3MLV)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:138 -L:197
5M:23 -M:88
6M:138 -M:197
7N:22 -N:92
8N:140 -N:196

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Tyr L:144 -Pro L:145
2Gly H:134 -Thr H:135
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Tyr M:144 -Pro M:145
6Phe N:146 -Pro N:147
7Glu N:148 -Pro N:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MLV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MLV)

(-) Exons   (0, 0)

(no "Exon" information available for 3MLV)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeeeeee.....eeeeeee...eeeee........eeeeeeee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlv H    1 EVQLVESGGEVKQPGQSLKISCKSSGYNFLDSWIGWVRQIPGKGLEWIGIIYPDDSDAHYSPSFEGQVTMSVDKSISTAYLQWTTLQASDTGKYFCTRLYLFEGAQSSNAFDLWGQGTMILVSSGTTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       134       144       154       164       174       184       194       204       214 
                                                                              52A                            82A||               100A||||||                         128|                                                                                 
                                                                                                              82B|                100B|||||                          134                                                                                 
                                                                                                               82C                 100C||||                                                                                                              
                                                                                                                                    100D|||                                                                                                              
                                                                                                                                     100E||                                                                                                              
                                                                                                                                      100F|                                                                                                              
                                                                                                                                       100G                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d3mlvl1 L:2-112 automated matches                                                                                    d3mlvl2 L:113-213 automated matches                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee.........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeeeeee......eeeeeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlv L    2 YLLTQPPSVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGKTATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGEGTRLTVLAQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  213
                                   |12        22        32        42        52        62        72        82        92   |||||96       106|      115       125       135       145       155       165       175       185       195       205        
                                   9|                                                                                  95A|||||        106A                                                                                                           
                                   11                                                                                   95B||||                                                                                                                       
                                                                                                                         95C|||                                                                                                                       
                                                                                                                          95D||                                                                                                                       
                                                                                                                           95E|                                                                                                                       
                                                                                                                            95F                                                                                                                       


Chain M from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3mlvm1 M:1-112 automated matches                                                                                     d3mlvm2 M:113-213 automated matches                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee.hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeeeee........eeeeee...eeeee........eeeee..hhhhhhh...eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee.hhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlv M    1 SYLLTQPPSVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGKTATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGEGTRLTVLAQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  213
                                    11        21        31        41        51        61        71        81        91    |||95F       105 |     114       124       134       144       154       164       174       184       194       204         
                                    9|                                                                                  95A|||||        106A                                                                                                           
                                    11                                                                                   95B||||                                                                                                                       
                                                                                                                          95C|||                                                                                                                       
                                                                                                                           95D||                                                                                                                       
                                                                                                                            95E|                                                                                                                       
                                                                                                                             95F                                                                                                                       


Chain N from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeeeeee.....eeeeeee...eeeee........eeeeeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhhhhh.eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlv N    1 EVQLVESGGEVKQPGQSLKISCKSSGYNFLDSWIGWVRQIPGKGLEWIGIIYPDDSDAHYSPSFEGQVTMSVDKSISTAYLQWTTLQASDTGKYFCTRLYLFEGAQSSNAFDLWGQGTMILVSSGTTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       134       144       154       164       174       184       194       204       214 
                                                                              52A                            82A||               100A||||||                         128|                                                                                 
                                                                                                              82B|                100B|||||                          134                                                                                 
                                                                                                               82C                 100C||||                                                                                                              
                                                                                                                                    100D|||                                                                                                              
                                                                                                                                     100E||                                                                                                              
                                                                                                                                      100F|                                                                                                              
                                                                                                                                       100G                                                                                                              


Chain P from PDB  Type:PROTEIN  Length:13
 aligned with Q79790_9HIV1 | Q79790 from UniProtKB/TrEMBL  Length:460

    Alignment length:13
                                   186   
        Q79790_9HIV1    177 RKRIRVGPGQTVY  189
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ...eeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                3mlv P  304 RKRIRVGPGQTVY  318
                                 ||315   
                               309|      
                                312      


Chain Q from PDB  Type:PROTEIN  Length:13
 aligned with Q79790_9HIV1 | Q79790 from UniProtKB/TrEMBL  Length:460

    Alignment length:13
                                   186   
        Q79790_9HIV1    177 RKRIRVGPGQTVY  189
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
           Pfam domains (1) GP120-3mlvQ01 Pfam domains (1)
           Pfam domains (2) GP120-3mlvQ02 Pfam domains (2)
         Sec.struct. author ...eeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                3mlv Q  304 RKRIRVGPGQTVY  318
                                 ||315   
                               309|      
                                312
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MLV)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: GP120] (26)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain P,Q   (Q79790_9HIV1 | Q79790)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu N:148 - Pro N:149   [ RasMol ]  
    Gly H:134 - Thr H:135   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe N:146 - Pro N:147   [ RasMol ]  
    Tyr L:144 - Pro L:145   [ RasMol ]  
    Tyr M:144 - Pro M:145   [ RasMol ]  
 
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  3mlv
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3MLV)

(-) Related Entries Specified in the PDB File

3mlr 3mls 3mlt 3mlu 3mlw 3mlx 3mly 3mlz